Hi,
I don't understand exactly follow what is going on here.
Are you entering mm coordinates into FSLView?
If the mapping from voxels of mm is not simple then it could be a rounding issue.
What happens if you shift the voxel coordinates forward and back (e.g. increase the X coordinate by one and then decrease it by one)? This should leave you in the same voxel but show you the exact mm coordinate for that voxel (otherwise you only see the rounded coordinates). If these still match but the intensity does not then there is a problem. If you see that the mm coordinates are now different then this would explain it.
Let us know what happens.
All the best,
Mark
On 18 Sep 2014, at 03:56, Xiuming Zhang (Eric) <[log in to unmask]> wrote:
> Hi Mark,
>
> Thanks a lot for replying!
>
> Yes, I have tried this before. It gave the same results as
> fslswapdim brain.nii.gz RL PA IS reorient.nii.gz
>
> That is, same RAS coordinates still give close but different intensity values in FSL and exactly the same intensity values in FreeSurfer.
>
> I think this could be probably because FSL rounds the RAS coordinates in a different way from FreeSurfer.
>
> Best regards,
> Xiuming
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